forked from OpenMS/OpenMS
-
Notifications
You must be signed in to change notification settings - Fork 0
/
CHANGELOG_PARAMS
308 lines (308 loc) · 31.9 KB
/
CHANGELOG_PARAMS
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
Tool name Added/removed Parameter name Type Default value Restrictions Supported formats
AssayGeneratorMetabo + ambiguity_resolution_mz_tolerance double 10.0
AssayGeneratorMetabo + ambiguity_resolution_mz_tolerance_unit string ppm ppm,Da
AssayGeneratorMetabo + ambiguity_resolution_rt_tolerance double 10.0
AssayGeneratorMetabo + consensus_spectrum_precursor_rt_tolerance double 5.0
AssayGeneratorMetabo + decoy_generation bool false
AssayGeneratorMetabo + decoy_generation_method string original original,resolve_overlap,add_shift,both
AssayGeneratorMetabo + fingerid:candidates int 10 1:
AssayGeneratorMetabo + fingerid:db string BIO
AssayGeneratorMetabo + fragment_annotation_score_threshold double 0.8 0.0:1.0
AssayGeneratorMetabo + max_transitions int 6
AssayGeneratorMetabo + preprocessing:precursor_mz_tolerance double 10.0
AssayGeneratorMetabo + preprocessing:precursor_mz_tolerance_unit string ppm Da,ppm
AssayGeneratorMetabo + preprocessing:precursor_rt_tolerance double 5.0
AssayGeneratorMetabo + project:ignore_formula bool false
AssayGeneratorMetabo + project:processors int 1
AssayGeneratorMetabo + project:q bool false
AssayGeneratorMetabo + sirius:candidates_per_ion int -1
AssayGeneratorMetabo + sirius:compound_timeout int 100 0:
AssayGeneratorMetabo + sirius:db string
AssayGeneratorMetabo + sirius:elements_considered string
AssayGeneratorMetabo + sirius:elements_enforced string
AssayGeneratorMetabo + sirius:formula string
AssayGeneratorMetabo + sirius:ions_considered string
AssayGeneratorMetabo + sirius:ions_enforced string
AssayGeneratorMetabo + sirius:no_isotope_filter bool false
AssayGeneratorMetabo + sirius:no_isotope_score bool false
AssayGeneratorMetabo + sirius:ppm_max double 10.0
AssayGeneratorMetabo + sirius:ppm_max_ms2 double 10.0
AssayGeneratorMetabo + sirius:profile string qtof default,qtof,orbitrap,fticr
AssayGeneratorMetabo + total_occurrence_filter double 0.1 0.0:1.0
AssayGeneratorMetabo - max_transitions int 3
AssayGeneratorMetabo - precursor_rt_tolerance double 5.0
AssayGeneratorMetabo - preprocessing:precursor_mz_tolerance double 5.0e-03
AssayGeneratorMetabo - preprocessing:precursor_mz_tolerance_unit string Da Da,ppm
AssayGeneratorMetabo - preprocessing:precursor_rt_tolerance int 5
AssayGeneratorMetabo - sirius:auto_charge bool false
AssayGeneratorMetabo - sirius:compound_timeout int 10 0:
AssayGeneratorMetabo - sirius:cores int 1 1:
AssayGeneratorMetabo - sirius:database string all all,chebi,custom,kegg,bio,natural products,pubmed,hmdb,biocyc,hsdb,knapsack,biological,zinc bio,gnps,pubchem,mesh,maconda
AssayGeneratorMetabo - sirius:elements string CHNOP[5]S[8]Cl[1]
AssayGeneratorMetabo - sirius:ion_tree bool false
AssayGeneratorMetabo - sirius:isotope string both score,filter,both,omit
AssayGeneratorMetabo - sirius:most_intense_ms2 bool false
AssayGeneratorMetabo - sirius:noise int 0 0:
AssayGeneratorMetabo - sirius:ppm_max int 10
AssayGeneratorMetabo - sirius:profile string qtof qtof,orbitrap,fticr
AssayGeneratorMetabo - sirius:top_n_hits int 10 1:
CometAdapter + enzyme string Trypsin Trypsin,Chymotrypsin,Lys-C,Lys-N,Asp-N,CNBr,PepsinA,unspecific cleavage,Trypsin/P,glutamyl endopeptidase,Arg-C
CometAdapter + second_enzyme string Trypsin,Chymotrypsin,Lys-C,Lys-N,Asp-N,CNBr,PepsinA,unspecific cleavage,Trypsin/P,glutamyl endopeptidase,Arg-C
CometAdapter - enzyme string Trypsin Arg-C,Trypsin,Asp-N,glutamyl endopeptidase,unspecific cleavage,Chymotrypsin,CNBr,Lys-C,Lys-N,PepsinA,Trypsin/P
CometAdapter - second_enzyme string Arg-C,Trypsin,Asp-N,glutamyl endopeptidase,unspecific cleavage,Chymotrypsin,CNBr,Lys-C,Lys-N,PepsinA,Trypsin/P
ConsensusID + PEPMatrix:matrix string PAM30MS identity,PAM30MS
ConsensusID - PEPMatrix:matrix string identity identity,PAM30MS
DecoyDatabase + enzyme string Trypsin Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Arg-C/P,Asp-N,Asp-N/B,Arg-C,staphylococcal protease/D,proline-endopeptidase/HKR,Formic_acid,Lys-C,no cleavage,unspecific cleavage,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Trypsin
DecoyDatabase - enzyme string Trypsin Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Trypsin,V8-DE,V8-E,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase
Digestor + enzyme string Trypsin glutamyl endopeptidase,Alpha-lytic protease,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Trypsin
Digestor - enzyme string Trypsin Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,glutamyl endopeptidase,Alpha-lytic protease,Trypsin,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR
DigestorMotif + enzyme string Trypsin 2-iodobenzoate,iodosobenzoate,Arg-C/P,Asp-N,Asp-N/B,Arg-C,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,Trypsin
DigestorMotif - enzyme string Trypsin cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,Trypsin,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P
FeatureFinderIdentification + EMGScoring:init_mom bool false
FeatureFinderIdentification + EMGScoring:max_iteration int 100 1:
FeatureFinderIdentification + extract:batch_size int 5000 1:
FeatureFinderIdentification + quantify_decoys bool false
FeatureFinderIdentification + svm:predictors string peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_ms1_isotope_correlation_score,var_ms1_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score
FeatureFinderIdentification - extract:batch_size int 1000 1:
FeatureFinderIdentification - svm:predictors string peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score
FeatureFinderMetaboIdent + EMGScoring:init_mom bool false
FeatureFinderMetaboIdent + EMGScoring:max_iteration int 100 1:
FeatureFinderMetaboIdent + debug int 0 0:
FeatureFinderMetaboIdent + detect:peak_width double 60.0 0.0:
FeatureFinderMetaboIdent - debug int 0
FeatureFinderMetaboIdent - detect:peak_width double 5.0 0.0:
FeatureLinkerUnlabeledQT + algorithm:min_IDscore_forTolCalc double 1.0
FeatureLinkerUnlabeledQT + algorithm:min_nr_diffs_per_bin int 50 5:
FeatureLinkerUnlabeledQT + algorithm:noID_penalty double 0.0 0.0:1.0
FileConverter + change_im_format string none none,concatenated,multiple_spectra,mixed
FileConverter + out output-file *.mzML,*.mzXML,*.cachedMzML,*.mgf,*.featureXML,*.consensusXML,*.edta,*.mzData,*.dta2d,*.csv,*.sqmass
FileConverter + out_type string mzML,mzXML,cachedMzML,mgf,featureXML,consensusXML,edta,mzData,dta2d,csv,sqmass
FileConverter - change_im_format string none none,multiple,single
FileConverter - out output-file *.mzML,*.mzXML,*.cachedMzML,*.mgf,*.featureXML,*.consensusXML,*.edta,*.mzData,*.dta2d,*.csv
FileConverter - out_type string mzML,mzXML,cachedMzML,mgf,featureXML,consensusXML,edta,mzData,dta2d,csv
FileInfo + in input-file *.mzData,*.mzXML,*.mzML,*.sqMass,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid,*.mzid,*.trafoXML,*.fasta,*.pqp
FileInfo + in_type string mzData,mzXML,mzML,sqMass,dta,dta2d,mgf,featureXML,consensusXML,idXML,pepXML,fid,mzid,trafoXML,fasta,pqp
FileInfo - in input-file *.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid,*.mzid,*.trafoXML,*.fasta,*.pqp
FileInfo - in_type string mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,idXML,pepXML,fid,mzid,trafoXML,fasta,pqp
GNPSExport + merged_spectra:cos_similarity double 0.9 0.0:
GNPSExport + merged_spectra:precursor_mass_tolerance double 0.5 0.0:
GNPSExport + ms2_bin_size double 0.019999999552965 0.0:
GNPSExport + output_type string most_intense merged_spectra,most_intense
GNPSExport + peptide_cutoff int 5 -1:
GNPSExport - merged_spectra:cos_similarity double 0.95
GNPSExport - output_type string full_spectra full_spectra,merged_spectra
GNPSExport - precursor_mz_tolerance double 1.0e-04
GNPSExport - precursor_rt_tolerance double 5.0
IDFileConverter + fasta_to_mzml:a_intensity double 1.0
IDFileConverter + fasta_to_mzml:add_a_ions bool false
IDFileConverter + fasta_to_mzml:add_abundant_immonium_ions bool false
IDFileConverter + fasta_to_mzml:add_all_precursor_charges bool false
IDFileConverter + fasta_to_mzml:add_b_ions string true true,false
IDFileConverter + fasta_to_mzml:add_c_ions bool false
IDFileConverter + fasta_to_mzml:add_first_prefix_ion bool false
IDFileConverter + fasta_to_mzml:add_losses bool false
IDFileConverter + fasta_to_mzml:add_metainfo bool false
IDFileConverter + fasta_to_mzml:add_precursor_peaks bool false
IDFileConverter + fasta_to_mzml:add_x_ions bool false
IDFileConverter + fasta_to_mzml:add_y_ions string true true,false
IDFileConverter + fasta_to_mzml:add_z_ions bool false
IDFileConverter + fasta_to_mzml:b_intensity double 1.0
IDFileConverter + fasta_to_mzml:c_intensity double 1.0
IDFileConverter + fasta_to_mzml:enzyme string Trypsin Arg-C,Chymotrypsin/P,CNBr,Formic_acid,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,TrypChymo,Trypsin/P,V8-DE,V8-E,no cleavage,unspecific cleavage,Lys-C,Lys-N,Lys-C/P,PepsinA,Trypsin
IDFileConverter + fasta_to_mzml:isotope_model string none none,coarse,fine
IDFileConverter + fasta_to_mzml:max_charge int 1
IDFileConverter + fasta_to_mzml:max_isotope int 2
IDFileConverter + fasta_to_mzml:max_isotope_probability double 0.05
IDFileConverter + fasta_to_mzml:min_charge int 1
IDFileConverter + fasta_to_mzml:missed_cleavages int 0
IDFileConverter + fasta_to_mzml:precursor_H2O_intensity double 1.0
IDFileConverter + fasta_to_mzml:precursor_NH3_intensity double 1.0
IDFileConverter + fasta_to_mzml:precursor_charge int 0
IDFileConverter + fasta_to_mzml:precursor_intensity double 1.0
IDFileConverter + fasta_to_mzml:relative_loss_intensity double 0.1
IDFileConverter + fasta_to_mzml:sort_by_position string true true,false
IDFileConverter + fasta_to_mzml:x_intensity double 1.0
IDFileConverter + fasta_to_mzml:y_intensity double 1.0
IDFileConverter + fasta_to_mzml:z_intensity double 1.0
IDFileConverter + in input-file *.pepXML,*.protXML,*.mascotXML,*.omssaXML,*.xml,*.psms,*.tsv,*.idXML,*.mzid,*.xquest.xml,*.fasta
IDFileConverter + out output-file *.idXML,*.mzid,*.pepXML,*.FASTA,*.xquest.xml,*.mzML
IDFileConverter + out_type string idXML,mzid,pepXML,FASTA,xquest.xml,mzML
IDFileConverter - in input-file *.pepXML,*.protXML,*.mascotXML,*.omssaXML,*.xml,*.psms,*.tsv,*.idXML,*.mzid,*.xquest.xml
IDFileConverter - out output-file *.idXML,*.mzid,*.pepXML,*.FASTA,*.xquest.xml
IDFileConverter - out_type string idXML,mzid,pepXML,FASTA,xquest.xml
IDFilter + best:n_spectra int 0 0:
IDFilter + blacklist:RegEx string
IDFilter + in_silico_digestion:enzyme string Trypsin Trypsin,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,no cleavage,unspecific cleavage,Arg-C/P,PepsinA,TrypChymo,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,V8-E,leukocyte elastase,proline endopeptidase,Trypsin/P,V8-DE,Arg-C,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,Asp-N,Asp-N/B
IDFilter + missed_cleavages:enzyme string Trypsin Trypsin,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,no cleavage,unspecific cleavage,Arg-C/P,PepsinA,TrypChymo,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,V8-E,leukocyte elastase,proline endopeptidase,Trypsin/P,V8-DE,Arg-C,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,Asp-N,Asp-N/B
IDFilter - in_silico_digestion:enzyme string Trypsin Trypsin,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Asp-N,Asp-N/B,leukocyte elastase,proline endopeptidase,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,Arg-C/P,Asp-N_ambic,Chymotrypsin,Arg-C,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate
IDFilter - missed_cleavages:enzyme string Trypsin Trypsin,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Asp-N,Asp-N/B,leukocyte elastase,proline endopeptidase,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,Arg-C/P,Asp-N_ambic,Chymotrypsin,Arg-C,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate
MSFraggerAdapter + digest:search_enzyme_name string Trypsin PepsinA,TrypChymo,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Lys-N,Lys-C/P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Formic_acid,Lys-C,Arg-C,Arg-C/P,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,no cleavage,unspecific cleavage,Trypsin
MSFraggerAdapter + license string yes,no
MSFraggerAdapter + search:localize_delta_mass int 0 0:
MSFraggerAdapter + tolerance:precursor_mass_tolerance_lower double 20.0 0.0:
MSFraggerAdapter + tolerance:precursor_mass_tolerance_upper double 20.0 0.0:
MSFraggerAdapter - digest:search_enzyme_name string Trypsin Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,glutamyl endopeptidase,Alpha-lytic protease,Trypsin,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR
MSFraggerAdapter - tolerance:precursor_mass_tolerance double 20.0 0.0:
MSSimulator + algorithm:MSSim:Digestion:enzyme string Trypsin Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,Trypsin
MSSimulator - algorithm:MSSim:Digestion:enzyme string Trypsin Trypsin,Arg-C,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,V8-DE,V8-E,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase
MascotAdapterOnline + Mascot_parameters:decoy bool false
MascotAdapterOnline + Mascot_server:batch_size int 50000 0:
MascotAdapterOnline - keep_protein_links bool false
MzTabExporter + export_all_psms bool false
NucleicAcidSearchEngine + oligo:enzyme string no cleavage RNase_T1,cusativin,RNase_H,mazF,colicin_E5,no cleavage,unspecific cleavage,RNase_U2,RNase_A,RNase_MC1
NucleicAcidSearchEngine - oligo:enzyme string no cleavage RNase_T1,cusativin,RNase_U2,RNase_A,RNase_MC1,RNase_H,no cleavage,unspecific cleavage
OMSSAAdapter + enzyme string Trypsin Trypsin,glutamyl endopeptidase,Lys-C/P,no cleavage,unspecific cleavage,CNBr,Formic_acid,Lys-C,Asp-N_ambic,Chymotrypsin,Asp-N,PepsinA,TrypChymo,Trypsin/P,Arg-C
OMSSAAdapter - enzyme string Trypsin Trypsin,CNBr,Formic_acid,Asp-N_ambic,Chymotrypsin,no cleavage,unspecific cleavage,glutamyl endopeptidase,Asp-N,Lys-C,Lys-C/P,Arg-C,PepsinA,TrypChymo,Trypsin/P
OpenPepXL + algorithm:number_top_hits int 1
OpenPepXL + fragment:mass_tolerance double 20.0
OpenPepXL + fragment:mass_tolerance_unit string ppm ppm,Da
OpenPepXL + fragment:mass_tolerance_xlinks double 20.0
OpenPepXL + modifications:variable_max_per_peptide int 3
OpenPepXL + peptide:enzyme string Trypsin Trypsin,Formic_acid,Lys-C,Lys-N,Asp-N,Asp-N/B,Asp-N_ambic,Lys-C/P,PepsinA,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,TrypChymo,Trypsin/P,V8-DE,V8-E,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,Arg-C/P,Chymotrypsin,Chymotrypsin/P,CNBr
OpenPepXL + peptide:missed_cleavages int 3
OpenPepXL + precursor:max_charge int 8
OpenPepXL + precursor:min_charge int 2
OpenPepXL - algorithm:number_top_hits int 5
OpenPepXL - fragment:mass_tolerance double 0.2
OpenPepXL - fragment:mass_tolerance_unit string Da ppm,Da
OpenPepXL - fragment:mass_tolerance_xlinks double 0.3
OpenPepXL - modifications:variable_max_per_peptide int 2
OpenPepXL - peptide:enzyme string Trypsin Trypsin,Arg-C/P,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,TrypChymo,Trypsin/P,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,Arg-C,Chymotrypsin,Chymotrypsin/P,CNBr,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Asp-N,Asp-N/B,Asp-N_ambic
OpenPepXL - peptide:missed_cleavages int 2
OpenPepXL - precursor:max_charge int 7
OpenPepXL - precursor:min_charge int 3
OpenPepXLLF + algorithm:number_top_hits int 1
OpenPepXLLF + modifications:variable_max_per_peptide int 3
OpenPepXLLF + peptide:enzyme string Trypsin Trypsin,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,unspecific cleavage,Arg-C,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin
OpenPepXLLF + peptide:missed_cleavages int 3
OpenPepXLLF + precursor:max_charge int 8
OpenPepXLLF + precursor:min_charge int 2
OpenPepXLLF - algorithm:number_top_hits int 5
OpenPepXLLF - modifications:variable_max_per_peptide int 2
OpenPepXLLF - peptide:enzyme string Trypsin Trypsin,Arg-C/P,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,TrypChymo,Trypsin/P,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,Arg-C,Chymotrypsin,Chymotrypsin/P,CNBr,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Asp-N,Asp-N/B,Asp-N_ambic
OpenPepXLLF - peptide:missed_cleavages int 2
OpenPepXLLF - precursor:max_charge int 7
OpenPepXLLF - precursor:min_charge int 3
OpenSwathAnalyzer + algorithm:EMGScoring:init_mom bool false
OpenSwathAnalyzer + algorithm:Scores:use_ionseries_scores string true true,false
OpenSwathAnalyzer + algorithm:Scores:use_ms2_isotope_scores string true true,false
OpenSwathRTNormalizer + algorithm:EMGScoring:init_mom bool false
OpenSwathRTNormalizer + algorithm:Scores:use_ionseries_scores string true true,false
OpenSwathRTNormalizer + algorithm:Scores:use_ms2_isotope_scores string true true,false
OpenSwathWorkflow + Scoring:EMGScoring:init_mom bool false
OpenSwathWorkflow + Scoring:Scores:use_ionseries_scores string true true,false
OpenSwathWorkflow + Scoring:Scores:use_ms2_isotope_scores string true true,false
PeptideIndexer + enzyme:name string auto auto,Lys-N,Lys-C/P,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Arg-C,Arg-C/P,Asp-N,Formic_acid,Lys-C,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,PepsinA,TrypChymo,Trypsin/P,V8-DE,Trypsin
PeptideIndexer - enzyme:name string auto auto,Asp-N,Asp-N/B,Asp-N_ambic,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Arg-C,Arg-C/P,Lys-C,Lys-N,Lys-C/P,PepsinA,Trypsin,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid
PercolatorAdapter + osw_level string ms2 ms1,ms2,transition
PercolatorAdapter - osw_level string ms2
ProteomicsLFQ + Alignment:align_algorithm:max_rt_shift double 0.1 0.0:
ProteomicsLFQ + Alignment:align_algorithm:min_run_occur int 2 2:
ProteomicsLFQ + Alignment:align_algorithm:min_score double 0.05
ProteomicsLFQ + Alignment:align_algorithm:score_cutoff bool false
ProteomicsLFQ + Alignment:align_algorithm:use_feature_rt string true true,false
ProteomicsLFQ + Alignment:align_algorithm:use_unassigned_peptides bool false
ProteomicsLFQ + Alignment:model:b_spline:boundary_condition int 2 0:2
ProteomicsLFQ + Alignment:model:b_spline:extrapolate string linear linear,b_spline,constant,global_linear
ProteomicsLFQ + Alignment:model:b_spline:num_nodes int 5 0:
ProteomicsLFQ + Alignment:model:b_spline:wavelength double 0.0 0.0:
ProteomicsLFQ + Alignment:model:interpolated:extrapolation_type string two-point-linear two-point-linear,four-point-linear,global-linear
ProteomicsLFQ + Alignment:model:interpolated:interpolation_type string cspline linear,cspline,akima
ProteomicsLFQ + Alignment:model:linear:symmetric_regression bool false
ProteomicsLFQ + Alignment:model:linear:x_datum_max double 1.0e15
ProteomicsLFQ + Alignment:model:linear:x_datum_min double 1.0e-15
ProteomicsLFQ + Alignment:model:linear:x_weight string 1/x,1/x2,ln(x),
ProteomicsLFQ + Alignment:model:linear:y_datum_max double 1.0e15
ProteomicsLFQ + Alignment:model:linear:y_datum_min double 1.0e-15
ProteomicsLFQ + Alignment:model:linear:y_weight string 1/y,1/y2,ln(y),
ProteomicsLFQ + Alignment:model:lowess:delta double -1.0
ProteomicsLFQ + Alignment:model:lowess:extrapolation_type string four-point-linear two-point-linear,four-point-linear,global-linear
ProteomicsLFQ + Alignment:model:lowess:interpolation_type string cspline linear,cspline,akima
ProteomicsLFQ + Alignment:model:lowess:num_iterations int 3 0:
ProteomicsLFQ + Alignment:model:lowess:span double 0.666666666666667 0.0:1.0
ProteomicsLFQ + Alignment:model:type string b_spline linear,b_spline,lowess,interpolated
ProteomicsLFQ + Alignment:model_type string b_spline linear,b_spline,lowess,interpolated
ProteomicsLFQ + Linking:min_IDscore_forTolCalc double 1.0
ProteomicsLFQ + Linking:min_nr_diffs_per_bin int 50 5:
ProteomicsLFQ + Linking:noID_penalty double 0.0 0.0:1.0
ProteomicsLFQ + PeptideQuantification:EMGScoring:init_mom bool false
ProteomicsLFQ + PeptideQuantification:EMGScoring:max_iteration int 100 1:
ProteomicsLFQ + PeptideQuantification:extract:batch_size int 5000 1:
ProteomicsLFQ + PeptideQuantification:quantify_decoys bool false
ProteomicsLFQ + PeptideQuantification:svm:predictors string peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_ms1_isotope_correlation_score,var_ms1_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score
ProteomicsLFQ + Seeding:charge string 2:5
ProteomicsLFQ + Seeding:intThreshold double 1.0e04
ProteomicsLFQ + Seeding:traceRTTolerance double 3.0
ProteomicsLFQ + alignment_order string star star,treeguided
ProteomicsLFQ + out_triqler output-file *.tsv
ProteomicsLFQ - Alignment:max_rt_shift double 0.1 0.0:
ProteomicsLFQ - Alignment:min_run_occur int 2 2:
ProteomicsLFQ - Alignment:min_score double 0.05
ProteomicsLFQ - Alignment:score_cutoff bool false
ProteomicsLFQ - Alignment:use_feature_rt string true true,false
ProteomicsLFQ - Alignment:use_unassigned_peptides bool false
ProteomicsLFQ - PeptideQuantification:extract:batch_size int 1000 1:
ProteomicsLFQ - PeptideQuantification:svm:predictors string peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score
ProteomicsLFQ - seedThreshold double 1.0e04
QCCalculator + address string
QCCalculator + description string
QCCalculator + label string label
QCCalculator + name string
QCCalculator + out output-file *.mzQC,*.qcML
QCCalculator + out_type string mzQC,qcML
QCCalculator - out output-file *.qcML
QualityControl + out_evd string
RNADigestor + enzyme string RNase_T1 RNase_T1,cusativin,RNase_U2,RNase_A,RNase_MC1,RNase_H,mazF,colicin_E5,no cleavage,unspecific cleavage
RNADigestor - enzyme string RNase_T1 RNase_T1,RNase_MC1,RNase_H,no cleavage,unspecific cleavage,cusativin,RNase_U2,RNase_A
RNPxlSearch + peptide:enzyme string Trypsin PepsinA,TrypChymo,Trypsin/P,Trypsin,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Asp-N,Asp-N/B,Asp-N_ambic,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,Arg-C/P,Lys-C,Lys-N,Lys-C/P,Arg-C,V8-DE,V8-E,leukocyte elastase,proline endopeptidase
RNPxlSearch - peptide:enzyme string Trypsin proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,Trypsin,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,no cleavage,unspecific cleavage,Lys-C,Lys-N,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Arg-C,Arg-C/P,V8-DE,V8-E,leukocyte elastase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR
SimpleSearchEngine + Search:annotate:PSM string ALL,fragment_mz_error_median_ppm,precursor_mz_error_ppm,matched_prefix_ions_fraction,matched_suffix_ions_fraction
SimpleSearchEngine + Search:enzyme string Trypsin Trypsin,Lys-C/P,PepsinA,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Lys-C,Lys-N,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Arg-C,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Asp-N,Asp-N/B,Asp-N_ambic,Arg-C/P,TrypChymo,Trypsin/P
SimpleSearchEngine - Search:annotate:PSM string fragment_mz_error_median_ppm,precursor_mz_error_ppm
SimpleSearchEngine - Search:enzyme string Trypsin Trypsin,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Lys-C/P,PepsinA,TrypChymo,Arg-C/P,Arg-C,unspecific cleavage,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,Lys-C,Lys-N,Chymotrypsin/P,CNBr,Formic_acid
SiriusAdapter + fingerid:candidates int 10 1:
SiriusAdapter + fingerid:db string BIO
SiriusAdapter + out_project_space string
SiriusAdapter + preprocessing:precursor_mz_tolerance double 10.0
SiriusAdapter + preprocessing:precursor_mz_tolerance_unit string ppm Da,ppm
SiriusAdapter + preprocessing:precursor_rt_tolerance double 5.0
SiriusAdapter + project:ignore_formula bool false
SiriusAdapter + project:processors int 1
SiriusAdapter + project:q bool false
SiriusAdapter + sirius:candidates_per_ion int -1
SiriusAdapter + sirius:compound_timeout int 100 0:
SiriusAdapter + sirius:db string
SiriusAdapter + sirius:elements_considered string
SiriusAdapter + sirius:elements_enforced string
SiriusAdapter + sirius:formula string
SiriusAdapter + sirius:ions_considered string
SiriusAdapter + sirius:ions_enforced string
SiriusAdapter + sirius:no_isotope_filter bool false
SiriusAdapter + sirius:no_isotope_score bool false
SiriusAdapter + sirius:ppm_max double 10.0
SiriusAdapter + sirius:ppm_max_ms2 double 10.0
SiriusAdapter + sirius:profile string qtof default,qtof,orbitrap,fticr
SiriusAdapter - out_workspace_directory string
SiriusAdapter - preprocessing:precursor_mz_tolerance double 5.0e-03
SiriusAdapter - preprocessing:precursor_mz_tolerance_unit string Da Da,ppm
SiriusAdapter - preprocessing:precursor_rt_tolerance int 5
SiriusAdapter - sirius:auto_charge bool false
SiriusAdapter - sirius:compound_timeout int 10 0:
SiriusAdapter - sirius:cores int 1 1:
SiriusAdapter - sirius:database string all all,chebi,custom,kegg,bio,natural products,pubmed,hmdb,biocyc,hsdb,knapsack,biological,zinc bio,gnps,pubchem,mesh,maconda
SiriusAdapter - sirius:elements string CHNOP[5]S[8]Cl[1]
SiriusAdapter - sirius:ion_tree bool false
SiriusAdapter - sirius:isotope string both score,filter,both,omit
SiriusAdapter - sirius:most_intense_ms2 bool false
SiriusAdapter - sirius:noise int 0 0:
SiriusAdapter - sirius:ppm_max int 10
SiriusAdapter - sirius:profile string qtof qtof,orbitrap,fticr
SiriusAdapter - sirius:top_n_hits int 10 1:
SpectraMerger + algorithm:sort_blocks string RT_ascending RT_ascending,RT_descending
SpectraMerger - algorithm:sort_blocks string RT_ascending RT_ascending, RT_descending
TextExporter + out output-file *.tsv,*.csv,*.txt
TextExporter + out_type string tsv,csv,txt
TextExporter - out output-file *.tsv
TextExporter - separator string
XTandemAdapter + enzyme string Trypsin PepsinA,TrypChymo,Trypsin/P,Trypsin,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,unspecific cleavage,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Arg-C/P,Lys-C,Lys-N,Lys-C/P,Arg-C,V8-DE,V8-E,leukocyte elastase
XTandemAdapter - enzyme string Trypsin Asp-N_ambic,Chymotrypsin,Trypsin,Formic_acid,Lys-C,Alpha-lytic protease,2-iodobenzoate,unspecific cleavage,Arg-C/P,Asp-N,Asp-N/B,Chymotrypsin/P,CNBr,Arg-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,glutamyl endopeptidase